I need help in selecting a restriction enzyme for GBS. Elshire's protocol for GBS calls for methylation-sensitive enzymes (They used ApeKI). He also underscores this in GBS workshops. I understand the use of methylation-sensitive REs is to filter out repetitive regions and to enrich genic regions, right?

Now here is where I am confused. I went out to search for literature for GBS done on insects (as I will be studying silkworm genomics), and found that some GBS studies use non-methylation-sensitive REs.

[1] Silva-Brandão et al in 2015, used PstI and MspI (double enzyme GBS) for oriental fruit moth. PstI and MspI are both NOT methylation sensitive.

[2] Dupuis et al in 2017 used PstI and MspI for GBS of the North American spruce budworm.

They both cited Poland 2012 for double digest GBS using PstI and MspI.

So does this mean methylation-sensitive REs are not required for GBS after all? What would be the consequences of choosing a methylation-insensitive vs. methylation-sensitive enzyme for GBS?